Since the Two Towers EE just came out today, I'm not sure which LOTR you're talking about, but since you're question fits the first movie's EE, you're either asking about that one or they're probably done the same way. If you look at the 2nd title, you should see that it has additional subtitle streams for the commentary tracks. If you uncheck the subtitle streams from that title that aren't in title 1, both titles are the same size. In other words, assuming you don't want to keep the extra subtitles, it shouldn't matter which one you keep.